File R-lfmm.spec of Package R-lfmm

# Automatically generated by CRAN2OBS
# 
# Spec file for package lfmm 
# This file is auto-generated using information in the package source, 
# esp. Description and Summary. Improvements in that area should be 
# discussed with upstream. 
# 
# Copyright (c) 2025 SUSE LINUX GmbH, Nuernberg, Germany. 
# 
# All modifications and additions to the file contributed by third parties 
# remain the property of their copyright owners, unless otherwise agreed 
# upon. The license for this file, and modifications and additions to the 
# file, is the same license as for the pristine package itself (unless the 
# license for the pristine package is not an Open Source License, in which 
# case the license is the MIT License). An "Open Source License" is a 
# license that conforms to the Open Source Definition (Version 1.9) 
# published by the Open Source Initiative. 
#  
# Please submit bugfixes or comments via http://bugs.opensuse.org/ 
# 
 
%global packname  lfmm 
%global rlibdir   %{_libdir}/R/library 
 
Name:           R-%{packname} 
Version:        1.1 
Release:        0 
Summary:        Latent Factor Mixed Models 
Group:          Development/Libraries/Other 
License:        GPL-3 
URL:            http://cran.r-project.org/web/packages/%{packname} 
Source:         lfmm_1.1.tar.gz 
Requires:       R-base 
Requires:	R-foreach
Requires:	R-rmarkdown
Requires:	R-knitr
Requires:	R-RSpectra
Requires:	R-ggplot2
Requires:	R-readr
Requires:	R-purrr
Requires:	R-Rcpp
Requires:	R-RcppEigen
Requires:	R-iterators
Requires:	R-cli
Requires:	R-gtable
Requires:	R-isoband
Requires:	R-lifecycle
Requires:	R-rlang
Requires:	R-S7
Requires:	R-scales
Requires:	R-vctrs
Requires:	R-withr
Requires:	R-evaluate
Requires:	R-highr
Requires:	R-xfun
Requires:	R-yaml
Requires:	R-magrittr
Requires:	R-clipr
Requires:	R-crayon
Requires:	R-hms
Requires:	R-R6
Requires:	R-tibble
Requires:	R-vroom
Requires:	R-cpp11
Requires:	R-tzdb
Requires:	R-bslib
Requires:	R-fontawesome
Requires:	R-htmltools
Requires:	R-jquerylib
Requires:	R-jsonlite
Requires:	R-tinytex
Requires:	R-base64enc
Requires:	R-cachem
Requires:	R-fastmap
Requires:	R-memoise
Requires:	R-mime
Requires:	R-sass
Requires:	R-glue
Requires:	R-pkgconfig
Requires:	R-digest
Requires:	R-farver
Requires:	R-labeling
Requires:	R-RColorBrewer
Requires:	R-viridisLite
Requires:	R-pillar
Requires:	R-bit64
Requires:	R-tidyselect
Requires:	R-progress
Requires:	R-bit
Requires:	R-utf8
Requires:	R-prettyunits
Requires:	R-fs
Requires:	R-rappdirs
 
# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse} 
# # Three others commonly needed 
# BuildRequires:  tex(ae.sty) 
# BuildRequires:  tex(fancyvrb.sty) 
# BuildRequires:  tex(inconsolata.sty) 
# BuildRequires:  tex(natbib.sty) 
# %else 
# BuildRequires:  texlive 
# %endif 
# BuildRequires:  texinfo 
BuildRequires:  fdupes 
BuildRequires:  R-base 
BuildRequires: 	R-foreach
BuildRequires: 	R-rmarkdown
BuildRequires: 	R-knitr
BuildRequires: 	R-RSpectra-devel
BuildRequires: 	R-ggplot2
BuildRequires: 	R-readr
BuildRequires: 	R-purrr
BuildRequires: 	R-Rcpp-devel
BuildRequires: 	R-RcppEigen-devel
BuildRequires: 	R-iterators
BuildRequires: 	R-cli
BuildRequires: 	R-gtable
BuildRequires: 	R-isoband
BuildRequires: 	R-lifecycle
BuildRequires: 	R-rlang
BuildRequires: 	R-S7
BuildRequires: 	R-scales
BuildRequires: 	R-vctrs
BuildRequires: 	R-withr
BuildRequires: 	R-evaluate
BuildRequires: 	R-highr
BuildRequires: 	R-xfun
BuildRequires: 	R-yaml
BuildRequires: 	R-magrittr
BuildRequires: 	R-clipr
BuildRequires: 	R-crayon
BuildRequires: 	R-hms
BuildRequires: 	R-R6
BuildRequires: 	R-tibble
BuildRequires: 	R-vroom
BuildRequires: 	R-cpp11-devel
BuildRequires: 	R-tzdb
BuildRequires: 	R-bslib
BuildRequires: 	R-fontawesome
BuildRequires: 	R-htmltools
BuildRequires: 	R-jquerylib
BuildRequires: 	R-jsonlite
BuildRequires: 	R-tinytex
BuildRequires: 	R-base64enc
BuildRequires: 	R-cachem
BuildRequires: 	R-fastmap
BuildRequires: 	R-memoise
BuildRequires: 	R-mime
BuildRequires: 	R-sass
BuildRequires: 	R-glue
BuildRequires: 	R-pkgconfig
BuildRequires: 	R-digest
BuildRequires: 	R-farver
BuildRequires: 	R-labeling
BuildRequires: 	R-RColorBrewer
BuildRequires: 	R-viridisLite
BuildRequires: 	R-pillar
BuildRequires: 	R-bit64
BuildRequires: 	R-tidyselect
BuildRequires: 	R-progress
BuildRequires: 	R-bit
BuildRequires: 	R-utf8
BuildRequires: 	R-prettyunits
BuildRequires: 	R-fs
BuildRequires: 	R-rappdirs
BuildRequires:  gcc gcc-c++ gcc-fortran
 
Suggests:	R-testthat
%description 
Fast and accurate inference of gene-environment associations (GEA) in 
genome-wide studies (Caye et al., 2019, <doi:10.1093/molbev/msz008>). 
We developed a least-squares estimation approach for confounder and 
effect sizes estimation that provides a unique framework for several 
categories of genomic data, not restricted to genotypes. The speed of 
the new algorithm is several times faster than the existing GEA 
approaches, then our previous version of the 'LFMM' program present in 
the 'LEA' package (Frichot and Francois, 2015, 
<doi:10.1111/2041-210X.12382>). 
 
%prep 
%setup -q -c -n %{packname} 
# the next line is needed, because we build without --clean in between two packages 
rm -rf ~/.R  
 
 
%build 
 
%install 
mkdir -p %{buildroot}%{rlibdir} 
%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} 
test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) 
rm -f %{buildroot}%{rlibdir}/R.css 
%fdupes -s %{buildroot}%{rlibdir} 
 
#%%check 
#%%{_bindir}/R CMD check %%{packname} 
 
%files 
%dir %{rlibdir}/%{packname} 
%doc %{rlibdir}/%{packname}/DESCRIPTION
%{rlibdir}/%{packname}/INDEX
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/data
%doc %{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%{rlibdir}/%{packname}/libs
 
%changelog